Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA - Archive ouverte HAL Access content directly
Journal Articles Journal of visualized experiments : JoVE Year : 2021

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

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Abstract

The growing role attributed nowadays to long non-coding RNAs (lncRNA) in physiology and pathophysiology makes it crucial to characterize their interactome by identifying their molecular partners, DNA, proteins and/or RNAs. The latter can interact with lncRNA through networks involving proteins, but they can also be engaged in direct RNA/RNA interactions. We, therefore, developed an easy-to-use RNA pull-down procedure that allowed identification of RNAs engaged in direct RNA/RNA interaction with a lncRNA using psoralen, a molecule that cross-links only RNA/RNA interactions. Bioinformatics modeling of the lncRNA secondary structure allowed the selection of several specific antisense DNA oligonucleotide probes with a strong affinity for regions displaying a low probability of internal base pairing. Since the specific probes that were designed targeted accessible regions throughout the length of the lncRNA, the RNA-interaction zones could be delineated in the sequence of the lncRNA. When coupled with a high throughput RNA sequencing, this protocol can be used for the whole direct RNA interactome studies of a lncRNA of interest.
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hal-03375987 , version 1 (26-10-2021)

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Audrey Jacq, Denis Becquet, Séverine Guillen, Bénédicte Boyer, Maria-Montserrat Bello-Goutierrez, et al.. Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA. Journal of visualized experiments : JoVE, 2021, 173, ⟨10.3791/62475⟩. ⟨hal-03375987⟩
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